The deep desulphurisation behaviour and steel cleanliness of stainless steel refining in the low sulphur content period (below 45 ppm [%S]) by using the current lime-fluorspar based slag and an optimized lime-alumina slag have been studied and compared. The desulphurisation effect was discussed based on the calculated sulphide capacity of slags and the equilibrated sulphur distribution ratio between the slag and steel. The sulphur evolution during the treatment was predicted with a previously developed kinetic model. The influence of slag chemistry on the compositional evolution of the steel and inclusions was discussed through thermodynamic considerations with respect to deoxidation and desulphurisation reactions. The sulphur content in the inclusions was predicted using the dissolved sulphur in the steel and their oxide chemistry. An equivalent steel cleanliness and desulphurisation effect was obtained with lime-alumina based slag as with lime-fluorspar based slag both in laboratory and industrial tests for low sulphur content stainless refining.